Re: preserving knees and shoulders....
I used to get sore shoulders after a day of pins (although it wouldn't seem painful during the pin itself). I found doing a few simple exercises to strengthen the muscles around my shoulders got rid of that problem.
Personally I find basic fitness really helps with ukemi. The muscles around a joint apparently play a role in protecting that joint.
The other thing I find helps me with eg not getting a sore back is stretching muscles right _after_ practicing.